BMC Medical Genetics
BioMed Central
Open Access
Research article
Deletions in the Y-derived amelogenin gene fragment in the Indian
population
VK Kashyap*1,2, Sanghamitra Sahoo1, T Sitalaximi1 and R Trivedi1
Address: 1National DNA Analysis Centre.Central Forensic Science Laboratory, Kolkata, INDIA and 2National Institute of Biologicals, A-32, Sector
62, Institutional Area, Noida 201307, Uttar Pradesh, India
Email: VK Kashyap* - vkk2k@hotmail.com; Sanghamitra Sahoo - sanghamitra_sahoo2001@yahoo.com; T Sitalaximi - ssita2k@yahoo.com;
R Trivedi - trivedi_r@hotmail.com
* Corresponding author
Published: 10 April 2006
BMC Medical Genetics2006, 7:37
doi:10.1186/1471-2350-7-37
Received: 21 November 2005
Accepted: 10 April 2006
This article is available from: http://www.biomedcentral.com/1471-2350/7/37
© 2006Kashyap et al; licensee BioMed Central Ltd.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Background: Rare failures in amelogenin-based gender typing of individuals have been observed
globally. In this study, we report the deletion of a large fragment of the amelogenin gene in 10
individuals out of 4,257 male samples analyzed from 104 different endogamous populations of India.
Methods: Samples were analyzed using commercial genetic profiling kits. Those that exhibited
failures in amelogenin-based gender identification were further analyzed with published as well as
newly designed primers to ascertain the nature and extent of mutation.
Results: The failure rate among Indian males was 0.23 %. Though the exact size and nature of the
deletion (single point mutations at a number of positions or a single large deletion) could not be
determined in the present study, it is inferred that the deletion spans a region downstream of the
reverse primer-binding site of commercially available amelogenin primer sets. Deletions were
conspicuously absent among the Mongoloid tribes of Northeast India, while both caste and tribal
groups harbored these mutations, which was predominantly among the Y-chromosomes belonging
to J2 lineage.
Conclusion: Our study indicates that the different amelogenin primer sets currently included in
genetic profiling multiplex kits may result in erroneous interpretations due to mutations
undetectable during routine testing. Further there are indications that these mutations could
possibly be lineage-specific, inherited deletions.
Background
Genotyping the X-Y homologous amelogenin gene segment for gender identification is widely used for DNA
profiling in DNA databasing, forensic casework, archeological specimens, preimplantation and prenatal diagnoses [1-4]. The amelogenin gene is a single copy gene,
homologues of which are located on Xp22.1-Xp22.3 and
Yp 11.2 [5]. Regions on this gene that are sufficiently conserved are amplified for simultaneous detection of the X
and Y alleles in gender identification procedures. Primers
bind to the first intron region of the amelogenin gene on
the X and Y-chromosomes [6] and amplify regions that
differ in base sequence, hence resulting in products that
are easily distinguishable by differences in size and
sequence. The most widely used primer set [6] delimits a
6 bp deletion on the X-chromosome and produces fragments of 106 bp and 112 bp for the X and Y chromosomes
respectively. Presence of two amplified products indicates
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provide evidence for a plausible inherited mode of transmission
of
the
mutation.
Methods
• Khatri
• Agharia
• Maratha
• Desasth Brahmin
• Khandayat
• Paroja
• Kuruva
• Iyengar
Brahmin
• Kallar
Population samples analyzed
DNA was isolated by standard organic extraction method
[12] either from blood or buccal swabs of consenting
4,257 male and 2,957 female individuals belonging to
104 different endogamous groups. Individuals represented major caste and tribal groups of India, which were
sampled from across 20 geographical regions of India
(Table 1, Figure 1).
• Vanniyar
Figure
Map
of
samples
depicting
1 where
the amelogenin
regions covered
deletion
in the
were
study
observed
and location
Map depicting the regions covered in the study and location
of samples where amelogenin deletion were observed.
a male genotype, while a single amplicon implies female
genotype. However, mutations in the Y-derived fragment
of the gene may result in amplification failure of the Yallele, causing misidentification of the biological sample
as of a female. Similarly, mutations on the X homologue
would also result in non-amplification of the X-derived
fragment although the genotype would still be identified
as male due to amplification of the Y-amelogenin allele.
Recently, a few studies have revealed misidentification of
the male genotype while employing the amelogenin gender test [[7-9]]. Failures in accurate determination of gender have been reported to be particularly high among
individuals of Indian origin. The frequency of failure was
observed to be 8 % by Santos et al. [7], while Thangaraj et
al. [9] reported 5 cases of amelogenin failure (1.85 %)
among the 270 Indian males studied. The failure rate of
the amelogenin sex test was particularly high (3.6 %) in
an Indian population group from Malaysia [10]. However, a parallel study testing a larger number of individuals from the Austrian National DNA database reported a
failure rate of 0.018 % [11]. The high frequency in incidence of failures in the Indian sub-continent prompted us
to scrutinize the amelogenin typing results of 7,214 individuals (including 4,257 males) belonging to 104 different endogamous populations that were genotyped as part
of our DNA databasing project. Individuals were sampled
from diverse geographic regions across India such that all
existing socio-ethnic groups and linguistic families were
represented. In this paper, we report failures in genotyping of male individuals due to mutations originating in
the Y-homologue of the amelogenin gene. We have further characterized the nature and extent of mutations and
Amelogenin typing using commercial genotyping kits
The DNA samples were amplified using commercial multiplex short tandem repeat (STR) kits; PowerPlex® 16 system (Promega Corporation, Madison, USA) and
Identifiler™ (Applied Biosystems, Foster City, CA), which
include the amelogenin marker for gender determination.
Genotyping of the amplified products was performed on
an ABI Prism™ 377 DNA Sequencer (PE Applied Biosystems, Foster City, CA). The amelogenin profile was determined from the electropherograms by comparing the
presence or absence of 106 and 112 bp peaks with known
male and female controls. Females exhibit a single peak of
106 bp while males exhibit two peaks of 106 and 112 bps.
Amelogenin typing using newly designed primers and other
published primers
Samples that showed abnormal amelogenin peak profiles
with the commercial kits were reamplified with primers
described by Steinlechner et al. [11] followed by genotyping as described above. Male samples exhibit two peaks of
219 and 225 bp, while female samples exhibit a single
peak at 219 bp.
Additional primers were designed for amplifying the
region identified by Roffey et al. [8] to decipher the origin
of mutations. The sequences of new primers designed to
facilitate detection of mutation are as follows:
1. #P1: 5'- TTACGGCCATATTTAGGA-3' (for amplification of X and Y homologues)
2. #P2: 5'- GAAAGAGTCAATCCGAATGGT-3' (for amplification of Y homologue)
Analysis of SRY, Y-STRs and Y-SNPs
To confirm the gender of the studied samples, a sex-determining locus (SRY) [13] specific to males, was amplified.
Occurrence of a single 93 bp amplicon would distinguish
an authentic male DNA sample from a female DNA sample. Further, four Y- short tandem repeats (Y-STRs)
[14,15] (DYS19, DYS389I, DYS389II and DYS390) were
amplified to determine the extent of deletion of the Y-
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Table 1: Incidences in failures of gender testing among the 104 endogamous populations of India tested for amelogerin gene efficacy
S.No
State
Population
Social Group
Individuals Tested
Failure in Gender Analysis
(No of samples)
1
Jammu & kashmir
2
3
Himachal Pradesh
Uttaranchal
4
Uttar Pradesh
5
Bihar
6
7
Gujarat
Maharastra
8
Chattisgarh
9
Jharkhand
10
Westbengal
11
Orrisa
12
Andhra Pradesh
Balti
Drokpa
Argon
Buddhist
HPRajput
Tharu
Jaunsari
Bhoksha
Kanyakubj Brahmin
UP Jat
UP Thakur
Khatri
UP Kurmi
Bihar Brahmin
Bhumihar
Rajput
Kayasth
Yadav
Kurmi
Baniya
Gujarat Patel
Desasth Brahmin
Chitpavan Brahmin
Maratha
Dhangar
Pawara
Katkari
Madia Gond
Mahadeo Koli
Brahmin
Satnami
Teli
Dheria Gond
Agharia
Oroan
Ho
Bhumij
Kharia
Munda
Birhor
Santhal
Oroan
Brahmin
Kayasth
Mahishya
Namasudra
Bauri
Maheli
Karmali
Kora
Lodha
Oriya Brahmin
Karan
Khandayat
Gope
Paroja
Juang
Saora
Andhra Brahmin
Tribe
Tribe
Tribe
Religious Group
Caste
Tribe
Tribe
Tribe
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Tribe
Tribe
Tribe
Tribe
Caste
Caste
Caste
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Caste
Caste
Caste
Caste
Caste
Tribe
Tribe
Tribe
Tribe
Caste
Caste
Caste
Caste
Tribe
Tribe
Tribe
Caste
67
38
51
156
50
45
45
42
98
48
48
47
45
59
65
58
53
44
50
45
45
70
78
65
150
82
95
45
45
51
50
50
35
70
42
50
56
83
64
61
61
60
110
103
60
55
54
49
51
59
99
57
62
62
60
78
50
35
106
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
1
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
1
Nil
1
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
1
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
1
Nil
1
Nil
Nil
Nil
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Table 1: Incidences in failures of gender testing among the 104 endogamous populations of India tested for amelogerin gene efficacy
13
Tamil Nadu
14
15
Kerala
Karnataka
16
Sikkim
17
Mizoram
18
19
Arunachal Pradesh
Manipur
20
Andaman & Nicobar
Islands
Raju
Kappu Naidu
Kamma Chaudhary
Reddy
Komati
Yerukula
Chenchu
Naikpod Gond
Lambadi
Golla
Sakunupakshollu
Chakkiliar
Tanjore Kallar
Vanniyar
Pallar
Gounder
Irular
Paraiyar
Nair
Iyenger Brahmin
Lingayat
Gowda
Bhovi
Christian
Muslim
Kuruva
Bhutia
Nepali
Lepcha
Mara
Hmar
Lai
Lusei
Kuki
Adi Pasi
Garo
Meitei
Naga
Hmar
Manipuri Muslim
Great Andamanese
Caste
Caste
Caste
Caste
Caste
Tribe
Tribe
Tribe
Tribe
Caste
Caste
Caste
Caste
Caste
Caste
Caste
Tribe
Caste
Caste
Caste
Caste
Caste
Caste
Religious Group
Religious Group
Tribe
Tribe
Caste
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Tribe
Religious Group
Tribe
66
104
106
107
104
101
100
104
107
65
30
49
101
87
33
56
54
21
87
65
98
56
52
55
65
60
75
110
48
90
80
92
92
105
203
110
105
106
101
101
24
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
1
1
Nil
Nil
Nil
Nil
Nil
1
Nil
Nil
Nil
Nil
Nil
1
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Nil
Jarawa
Onge
Nicobarese
Shompen
Tribe
Tribe
Tribe
Tribe
50
16
28
33
Nil
Nil
Nil
Nil
* NUMBER OF POPULATIONS ANALYZED: 104; 4257 MALES OUT OF 7214 INDIVIDUALS ANALYZED IN GENETIC PROFILING
chromosome and to determine if Y-STR haplotype profiles were shared between individuals. Y-STR amplification was carried out in a single tube multiplex reaction
[14] and genotyped on an ABI Prism™ 377 DNA
Sequencer (PE Applied Biosystems, Foster City, CA). Ysingle nucleotide polymorphisms (Y-SNPs) (M89, M9,
M172, 92R7, M45, M20, M70, M214, M69, M124, M173,
M17) [16] were profiled hierarchically to identify the lineage of the test samples.
Results and Discussion
Out of the 4,257 males analyzed with either PowerPlex®
16 or Identifiler™ multiplex system, 10 confirmed male
samples exhibited a dropout of the 112 bp amelogenin Yallele (Table 1). To verify the cause of observed abnormalities, we tested such samples with alternate primer pairs
that encompassed the region amplified with primers
reported by Sullivan et al. [6] and, are also typically used
in the commercial kits. Amplification of the test samples
with the primer set described by Steinlechner et al. [11]
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Table 2: Y-chromosome profiles of the amelogenin-deletion individuals*
S. No
Sample
1
2
3
4
5
6
7
8
9
10
Kallar
Vanniyar
Agharia
Khatri
Iyenger Brahmin
Kuruva
Khandayat
Paroja
Desasth Brahmin
Maratha
Y-SNP
DYS 19
DYS 389I
DYS 389II
DYS 390
NA
J2
NA
NA
J2
NA
J2
J2
J2
J2
15
15
15
15
14
15
15
15
14
15
12
13
12
13
13
13
11
13
13
11
29
29
29
30
29
30
30
26
30
28
25
24
25
25
24
25
23
25
23
25
NA: Samples not be examined for Y-SNPs
* Integers in bold represent shared haplotype between Kallar and Agahria; while those in bold italics represent haploype sharing between Khatri and
Kuruva
resulted in complete absence of the 225 bp Y-specific
product.
All 10 ambiguous samples were confirmed to be from
male individuals on testing with male-specific SRY locus,
which yielded the characteristic 93 bp amplicon reconfirming the gender of these subjects as males.
Additional analysis with four Y-chromosomal STR markers, DYS19, DYS389I, DYS389II and DYS390, yielded
complete and different Y-STR haplotype profiles. Amplification of Y-STR indicates that these samples had failed the
amelogenin typing either due to mutation in the primerbinding region [17] or due to deletions in the amelogenin
region (11.2p) on the Y-chromosome [11]. Among the 10
samples, eight distinct Y-STR haplotype profiles were
observed; one was shared between Khatri and Kuruva and,
another one by Agharia and Kallar (Table 2). Further
amplification and sequencing was carried out using the
forward primer of Steinlechner et al. [11] and a set of
newly designed reverse primers spanning the hypothetical
region of mutation – #P1, which is 62 bp downstream,
and #P2, a Y-specific primer that is 43 bp downstream to
the Steinlechner's reverse primer binding region, in order
to determine the nature and extent of mutation. The
newly designed primers depicted in Fig.2, result in 287 bp
and 268 bp amplicon for #P1 and #P2 respectively, for the
Y-chromosome, when used along with the forward primer
of Steinlechner et al., #P1 results in a 281 bp product for
the X-chromosome. However, the newly designed and
validated primer sets also failed to amplify the Y-homologue in test samples suggesting deletion of a significant
portion of the amelogenin region in male samples. The
deletion in amelogenin gene has recently been mapped to
span around 2.5 Mb [18].
The overall rate of failure among the Indian population
was found to be 0.23%. Table 1 shows the frequency of
failure among different endogamous groups. Failures
were exhibited by both caste groups (Khatri, Desasth
Brahmin, Maratha, Khandayat, Tanjore Kallar, Vanniyar
and Iyenger Brahmin) and tribal populations (Agharia,
Paroja, and Kuruva) while Mongoloid and Negrito populations were not found to harbor the deletions (Fig. 1).
Interestingly, we observed that these deletions were
present predominantly in individuals belonging to the J2
Y-chromosomal lineage. J2 is found in approximately
5.1% of the Indian population, while majority of the
Indian males harbor H (25%), R1a1 (19%) and R2 (16%)
haplogroups in their Y-chromosomes [19]. Probably originating in the Middle East [20], the J2 lineage has been
found distributed across southeastern Europe and Asia
with frequencies of 6.5% in Central Asians [16], 23.8% in
Sephardic Jews, 20% in Lebanese, 17.8% in Konyan
Turks, 16.3% among Italians of Apulia, 13.6% in French
Basque [20], 10.2% in Moroccan Arabs [21]. The above
observations and positive amplification of the SRY gene
and the appearance of discrete Y-STR haplotypes, suggests
that the mutations probably arose independently on a J2
Y chromosome lineage background.
Of the endogamous populations screened in this study,
~10 % exhibited failures in the amelogenin gender test.
Since the extent of deletion is large to avoid amplification
dropout of the Y-homologue with currently available
commercial primer sets, we suggest it would be prudent to
include an additional gender test such as SRY and/or YSTR testing for accurate gender identification of biological
specimens.
Conclusion
Earlier studies have reported high failure rates in amelogenin-based gender testing of individuals from the Indian
sub-continent. In this study, we have analyzed 4,257 male
samples and report a failure rate of 0.23%. Due to ease of
typing, this test has gained wide acceptance and has been
integrated into routine automated genetic profiling procedures. However, the fallibility of the amelogenin test
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Steinlechner Forward Primer
Sullivan Forward Primer
Sullivan Reverse Primer
Steinlechner Reverse Primer
Y-specific Primer
Universal Primer
Figure
Y-chromosome
tion of annealing
2
nucleotide
regions of sequence
the primerofsets
the used
human
in amelogenin
this study gene (GenBank Accession Number M55419) showing the locaY-chromosome nucleotide sequence of the human amelogenin gene (GenBank Accession Number M55419) showing the location of annealing regions of the primer sets used in this study.
raises concern over its continued use especially in medical
and forensic sciences.
Although our study indicates that individuals belonging
to the J2 lineage are more prone to deletion in Y-derived
amelogenin gene, further corroborating studies are
desired. The amelogenin-based gender test thus needs to
be applied with caution, with supplementation with other
Y-chromosome specific analyses for reliable gender identification.
Competing interests
The author(s) declare that they have no competing interests.
Authors' contributions
VKK conceptualized the study and contributed significantly in data interpretation and manuscript preparation.
SS and TS contributed equally towards designing and carrying out of experiments, data analyses and in manuscript
preparation. RT provided critical and valuable information for data processing. All authors read and approved
the final manuscript.
Acknowledgements
This study was supported by a research grant under the X Five Year Plan
to CFSL, Kolkata. The authors are thankful to Rajkumar R, Gaikwad S,
Sarkar N, Tandon M, Guha S, Maity B, Ashma R, Banerjee J, Singh A and G.
Hima Bindu, research scholars of the National DNA Analysis Centre, Kolkata and S. Krittika, JRF (Indian Statistical Institute, Kolkata) for providing
their data for use in this study. We also thank the two reviewers for their
valuable suggestions. SS and ST were assisted with MHA and CSIR fellowships, respectively.
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